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Solodneva E, Svishcheva G, Smolnikov R, Bazhenov S, Konorov E, Mukhina V, Stolpovsky Y. Genetic Structure Analysis of 155 Transboundary and Local Populations of Cattle ( Bos taurus, Bos indicus and Bos grunniens) Based on STR Markers. Int J Mol Sci 2023; 24:5061. [PMID: 36902492 PMCID: PMC10003406 DOI: 10.3390/ijms24055061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 03/09/2023] Open
Abstract
Every week, 1-2 breeds of farm animals, including local cattle, disappear in the world. As the keepers of rare allelic variants, native breeds potentially expand the range of genetic solutions to possible problems of the future, which means that the study of the genetic structure of these breeds is an urgent task. Providing nomadic herders with valuable resources necessary for life, domestic yaks have also become an important object of study. In order to determine the population genetic characteristics, and clarify the phylogenetic relationships of modern representatives of 155 cattle populations from different regions of the world, we collected a large set of STR data (10,250 individuals), including unique native cattle, 12 yak populations from Russia, Mongolia and Kyrgyzstan, as well as zebu breeds. Estimation of main population genetic parameters, phylogenetic analysis, principal component analysis and Bayesian cluster analysis allowed us to refine genetic structure and provided insights in relationships of native populations, transboundary breeds and populations of domestic yak. Our results can find practical application in conservation programs of endangered breeds, as well as become the basis for future fundamental research.
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Affiliation(s)
- Evgenia Solodneva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
| | - Gulnara Svishcheva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Rodion Smolnikov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
| | - Sergey Bazhenov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
| | - Evgenii Konorov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
- Gorbatov Federal Research Center for Food Systems, Russian Academy of Sciences, 109316 Moscow, Russia
| | - Vera Mukhina
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
| | - Yurii Stolpovsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
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2
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Aitnazarov RB, Mishakova TM, Yudin NS. Assessment of genetic diversity and phylogenetic relationships in Black Pied cattle in the Novosibirsk Region using microsatellite markers. Vavilovskii Zhurnal Genet Selektsii 2022; 25:831-838. [PMID: 35088018 PMCID: PMC8761576 DOI: 10.18699/vj21.096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/17/2021] [Accepted: 10/17/2021] [Indexed: 12/02/2022] Open
Abstract
There are currently over a thousand indigenous cattle breeds well adapted to local habitat conditions thanks
to their long history of evolution and breeding. Identification of the genetic variations controlling the adaptation of
local cattle breeds for their further introduction into the genome of highly productive global breeds is a matter of great
relevance. Studying individual populations of the same breed with the use of microsatellite markers makes it possible
to assess their genetic diversity, relationships, and breed improvement potential. Although the Black Pied breed is the
most common dairy cattle breed in Russia, there are only a few studies on genetic diversity in local Black Pied populations
in some Russian regions. The goal of the present study was to analyze the genetic diversity in Black Pied cattle
populations in the Novosibirsk Region and compare them with other Russian populations; to identify significantly divergent
populations with a view to preserving them under the programs aimed at maintaining the genetic diversity of
the domestic Black Pied breed. DNA samples from 4788 animals of the Black Pied breed from six breeding enterprises
in the Novosibirsk Region have been studied using 11 microsatellite markers. No significant differences in genetic
variability parameters were found between individual populations. Private alleles have been identified in five out of
six populations. Five populations have shown inbreeding coefficient values (FIS) below zero, which indicates heterozygosity
excess. The population distribution test, principal component analysis, FST and DEST values, cluster analysis,
and phylogenetic analysis have revealed two populations genetically distinct from the others. Essentially, the genetic
diversity parameters of the six studied Black Pied cattle populations from the Novosibirsk Region show no significant
differences from other Russian populations of the breed. Excess heterozygosity is observed in most breeding enterprises,
which is a sign of a low inbreeding rate. To maintain the genetic diversity of the Russian Black Pied cattle, we
recommend focusing on the two populations with significant genetic distinctions from the others.
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Affiliation(s)
- R. B. Aitnazarov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - T. M. Mishakova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - N. S. Yudin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
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3
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Gamarra D, Taniguchi M, Aldai N, Arakawa A, Lopez-Oceja A, de Pancorbo MM. Genetic Characterization of the Local Pirenaica Cattle for Parentage and Traceability Purposes. Animals (Basel) 2020; 10:E1584. [PMID: 32899488 PMCID: PMC7552125 DOI: 10.3390/ani10091584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 08/23/2020] [Accepted: 09/03/2020] [Indexed: 11/26/2022] Open
Abstract
Pirenaica is the most important autochthonous cattle breed within the Protected Geographic Indication (PGI) beef quality label in the Basque region, in northern Spain. The short tandem repeats (STRs) are powerful markers to elucidate forensic cases and traceability across the agri-food sector. The main objective of the present work was to study the phylogenetic relationships of Pirenaica cattle and other breeds typically raised in the region and provide the minimum number of STR markers for parentage and traceability purposes. The 30-STR panel recommended by the International Society of Animal Genetics-Food and Agriculture Organization of the United Nations (ISAG-FAO) was compared against other commercial STR panels. The 30-STR panel showed a combined matching probability of 1.89 × 10-25 and a power of exclusion for duos of 0.99998. However, commercial STR panels showed a limited efficiency for a reliable parentage analysis in Pirenaica, and at least a 21-STR panel is needed to reach a power of exclusion of 0.9999. Machine-learning analysis also demonstrated a 95% accuracy in assignments selecting the markers with the highest FST in Pirenaica individuals. Overall, the present study shows the genetic characterization of Pirenaica and its phylogeny compared with other breeds typically raised in the Basque region. Finally, a 21-STR panel with the highest FST markers is proposed for a confident parentage analysis and high traceability.
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Affiliation(s)
- David Gamarra
- Biomics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain; (D.G.); (A.L.-O.)
| | - Masaaki Taniguchi
- Animal Genome Unit, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO), Tsukuba 305-0901, Japan; (M.T.); (A.A.)
| | - Noelia Aldai
- Lactiker Research Group, Department of Pharmacy and Food Sciences, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain;
| | - Aisaku Arakawa
- Animal Genome Unit, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO), Tsukuba 305-0901, Japan; (M.T.); (A.A.)
| | - Andres Lopez-Oceja
- Biomics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain; (D.G.); (A.L.-O.)
| | - Marian M. de Pancorbo
- Biomics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain; (D.G.); (A.L.-O.)
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4
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Nonhuman forensic genetics. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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5
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Mukherjee S, Singh P, Tuccia F, Pradelli J, Giordani G, Vanin S. DNA characterization from gut content of larvae of Megaselia scalaris (Diptera, Phoridae). Sci Justice 2019; 59:654-659. [DOI: 10.1016/j.scijus.2019.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/10/2019] [Accepted: 06/02/2019] [Indexed: 11/24/2022]
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Moore MK, Frazier K. Humans Are Animals, Too: Critical Commonalities and Differences Between Human and Wildlife Forensic Genetics. J Forensic Sci 2019; 64:1603-1621. [DOI: 10.1111/1556-4029.14066] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 03/10/2019] [Accepted: 04/08/2019] [Indexed: 12/31/2022]
Affiliation(s)
- M. Katherine Moore
- Forensic Laboratory Conservation Biology Division Northwest Fisheries Science Center, National Marine Fisheries Service National Oceanic and Atmospheric Administration 219 Fort Johnson Road Charleston SC29412
| | - Kim Frazier
- Wyoming Game and Fish Wildlife Forensic and Fish Health Laboratory 1212 South Adams Street Laramie WY 82070
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Shang S, Zhang M, Zhao Y, Dang W, Hua P, Zhang S, Wang Z. Development and validation of a novel 13‐plex
PCR
system for commonly used short tandem repeats in horses (
Equus caballus
). Equine Vet J 2018; 51:688-695. [DOI: 10.1111/evj.13047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 11/13/2018] [Indexed: 11/30/2022]
Affiliation(s)
- S. Shang
- Institute of Equine Sciences College of Animal Science and Veterinary Medicine Shenyang Agricultural University Shenyang PR China
- College of Food Science Shenyang Agricultural University Shenyang PR China
| | - M. Zhang
- College of Economics and Management Shenyang Agricultural University Shenyang PR China
| | - Y. Zhao
- Institute of Equine Sciences College of Animal Science and Veterinary Medicine Shenyang Agricultural University Shenyang PR China
| | - W. Dang
- Institute of Equine Sciences College of Animal Science and Veterinary Medicine Shenyang Agricultural University Shenyang PR China
| | - P. Hua
- School of Ecological and Environmental Sciences East China Normal University Shanghai PR China
| | - S. Zhang
- Institute of Equine Sciences College of Animal Science and Veterinary Medicine Shenyang Agricultural University Shenyang PR China
| | - Z. Wang
- Institute of Equine Sciences College of Animal Science and Veterinary Medicine Shenyang Agricultural University Shenyang PR China
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8
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Genetic characterization and founder effect analysis of recently introduced Salers cattle breed population. Animal 2016; 11:24-32. [PMID: 27278345 DOI: 10.1017/s1751731116001063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Salers are a native French breed used for beef and dairy production that has expanded to all the continents. The Salers breed was introduced to the north of Spain in 1985 with only 15 individuals from France and has successfully increased to over 20 000 animals. Although over time new animals have been imported from France for breeding, it is possible that the limiting number of founder animals could have resulted in a reduction of the genetic diversity found in Spanish Salers. Thus, the purpose of the present study has been to characterize the genetic diversity of Salers breed in Spain and evaluate a possible founder effect due to reduced number of the first reproducers. A total of 403 individuals from 12 Salers herds were analyzed using 12 microsatellite markers and compared with phylogenetically and geographically close related Blonde d'Aquitaine, Limousin and Charolais French breeds but also other 16 European breeds. Microsatellites in Salers were polymorphic, with a mean allelic richness of 5.129 and an expected heterozygosity of 0.621 across loci (0.576 to 0.736 among all breeds). Average observed heterozygosity was 0.618. All the loci fit the Hardy-Weinberg (HW) equilibrium except TGLA227 locus due to a significant deficit of heterozygotes in only one of the herds, probably attributable to a sampling effect. When all loci were combined, Salers inbreeding coefficient did not differ statistically from 0 (F IS=0.005), indicating not significant excess or deficit of heterozygotes (P=0.309). Based in allelic distribution, Salers revealed a frequency of 0.488 in BM2113-131 and 0.064 in BM2113-143 diagnostic alleles, which are specific to the African zebu. These zebu alleles are also found in some French breeds, supported by STR data previously postulated hypothesis of a migration route through Mediterranean route by which North African cattle may have left a genetic signature in southern Europe. Phylogenetic tree and population structure analyses could unambiguously differentiate Salers cattle from the other populations and 10% of the total genetic variability could be attributed to differences among breeds (mean R ST=0.105; P<0.01). Mutation-drift equilibrium tests (sign test and Wilcoxon's sign rank test) were in correspondence to the absence of founder effect when Bonferroni was applied. Gene diversity previously reported in French Salers was comparable with the observed in our population. Thus, high genetic diversity in Spanish Salers highlights the resources of this population, which looks toward future breeding and selection programs.
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9
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Kanthaswamy S. Review: domestic animal forensic genetics - biological evidence, genetic markers, analytical approaches and challenges. Anim Genet 2015; 46:473-84. [DOI: 10.1111/age.12335] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2015] [Indexed: 01/09/2023]
Affiliation(s)
- S. Kanthaswamy
- School of Mathematical and Natural Sciences; Arizona State University (ASU) at the West Campus; 4701 W Thunderbird Road Glendale AZ 85306-4908 USA
- California National Primate Research Center; University of California; Davis CA 95616 USA
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10
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Agerholm JS, Holm W, Schmidt M, Hyttel P, Fredholm M, McEvoy FJ. Perosomus elumbis in Danish Holstein cattle. BMC Vet Res 2014; 10:227. [PMID: 25253618 PMCID: PMC4181705 DOI: 10.1186/s12917-014-0227-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 09/20/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Perosomus elumbis (PE) is a congenital defect that has been observed sporadically in Holstein cattle for many years. However, several cases have been reported in recent years and this may indicate an unrecognised spread of a mutant allele in the Holstein population worldwide. Two cases in Danish Holstein calves are reported to provide details on the phenotype. CASE PRESENTATION Two full-term Holstein calves were born after assisted delivery due to dystocia with breech presentation. External morphological examination indicated that the lumbar, sacral and coccygeal vertebrae were absent and the abdominal region was just present as a floppy sac covered by skin and enclosing the abdominal organs. The hind limbs were hypoplastic with bilateral symmetric arthrogryposis and muscular atrophy. Radiographs, computed tomography scan and necropsy confirmed these findings. The caudal part of the thoracic spinal cord showed myelodysplasia. A range of abdominal organ malformations were found at necropsy. Inbreeding was not found during genealogical examination, but remote shared ancestors were present in the pedigrees. CONCLUSION The addition of these further cases of PE to the in recent years reported record of cases should draw more attention to this defect in the Holstein breed. PE may be an emerging genetic defect in the Holstein population worldwide and cases should be sampled to enable genetic mapping of the gene possibly underlying the disease. PE cases seem to be associated with a high risk of dystocia due to increased rate of breech presentation.
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11
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Foreign meat identification by DNA breed assignment for the Chinese market. Meat Sci 2014; 98:822-7. [PMID: 25170818 DOI: 10.1016/j.meatsci.2014.07.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 07/03/2014] [Accepted: 07/26/2014] [Indexed: 11/22/2022]
Abstract
Methods for individual identification are usually employed for traceability, whereas breed identification is useful to detect commercial frauds. In this study, Chinese Yellow Cattle (CYC) samples plus data from six Bos taurus breeds, two Bos indicus breeds, and one composite breed were used to develop an allocation test based on 22 microsatellites. The test allowed discriminating all foreign breeds from the CYC, although some CYC individuals were wrongly allocated as Limousin or Holstein, probably due to the recent introduction of these breeds into China. In addition, CYC evidenced a previously reported Zebu cline (south-north) and a possible structure within the B. taurus component that should be confirmed. An independent test performed with meat samples of unknown breed origin from Argentina allocated 92% of them to either Angus, Hereford, or their crossbreed, but none was identified as CYC. We conclude that the test is a suitable tool to certify meat of foreign breed origin and to detect adulterations of CYC beef labeled as imported meat.
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12
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Fernández ME, Rogberg-Muñoz A, Lirón JP, Goszczynski DE, Ripoli MV, Carino MH, Peral-García P, Giovambattista G. Effectiveness of single-nucleotide polymorphisms to investigate cattle rustling. J Forensic Sci 2014; 59:1607-13. [PMID: 25039316 DOI: 10.1111/1556-4029.12562] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 10/05/2013] [Accepted: 10/26/2013] [Indexed: 11/26/2022]
Abstract
Short tandem repeats (STR)s have been the eligible markers for forensic animal genetics, despite single-nucleotide polymorphisms (SNP)s became acceptable. The technology, the type, and amount of markers could limit the investigation in degraded forensic samples. The performance of a 32-SNP panel genotyped through OpenArrays(TM) (real-time PCR based) was evaluated to resolve cattle-specific forensic cases. DNA from different biological sources was used, including samples from an alleged instance of cattle rustling. SNPs and STRs performance and repeatability were compared. SNP call rate was variable among sample type (average = 80.18%), while forensic samples showed the lowest value (70.94%). The repeatability obtained (98.7%) supports the used technology. SNPs had better call rates than STRs in 12 of 20 casework samples, while forensic index values were similar for both panels. In conclusion, the 32-SNPs used are as informative as the standard bovine STR battery and hence are suitable to resolve cattle rustling investigations.
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Affiliation(s)
- María E Fernández
- Instituto de Genética Veterinaria (IGEVET), CCT La Plata - CONICET - Fac Cs Veterinarias, UNLP, 60 Y 118 S/N, 1900, La Plata, Argentina
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13
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Banks MA, Jacobson DP, Meusnier I, Greig CA, Rashbrook VK, Ardren WR, Smith CT, Bernier‐Latmani J, Van Sickle J, O'Malley KG. Testing advances in molecular discrimination among Chinook salmon life histories: evidence from a blind test. Anim Genet 2014; 45:412-20. [PMID: 24628286 PMCID: PMC4112815 DOI: 10.1111/age.12135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2014] [Indexed: 11/29/2022]
Abstract
The application of DNA-based markers toward the task of discriminating among alternate salmon runs has evolved in accordance with ongoing genomic developments and increasingly has enabled resolution of which genetic markers associate with important life-history differences. Accurate and efficient identification of the most likely origin for salmon encountered during ocean fisheries, or at salvage from fresh water diversion and monitoring facilities, has far-reaching consequences for improving measures for management, restoration and conservation. Near-real-time provision of high-resolution identity information enables prompt response to changes in encounter rates. We thus continue to develop new tools to provide the greatest statistical power for run identification. As a proof of concept for genetic identification improvements, we conducted simulation and blind tests for 623 known-origin Chinook salmon (Oncorhynchus tshawytscha) to compare and contrast the accuracy of different population sampling baselines and microsatellite loci panels. This test included 35 microsatellite loci (1266 alleles), some known to be associated with specific coding regions of functional significance, such as the circadian rhythm cryptochrome genes, and others not known to be associated with any functional importance. The identification of fall run with unprecedented accuracy was demonstrated. Overall, the top performing panel and baseline (HMSC21) were predicted to have a success rate of 98%, but the blind-test success rate was 84%. Findings for bias or non-bias are discussed to target primary areas for further research and resolution.
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Affiliation(s)
- Michael A. Banks
- Coastal Oregon Marine Experiment StationDepartment of Fisheries and WildlifeHatfield Marine Science CenterOregon State UniversityNewportOR97365USA
| | - David P. Jacobson
- Coastal Oregon Marine Experiment StationDepartment of Fisheries and WildlifeHatfield Marine Science CenterOregon State UniversityNewportOR97365USA
| | - Isabelle Meusnier
- Center for Biology and Management of PopulationsMontpellier34000France
| | - Carolyn A. Greig
- Department of BiosciencesCollege of ScienceSwansea UniversitySwanseaWalesSA1 1LGUK
| | - Vanessa K. Rashbrook
- UC Davis Genome Center – DNA Technologies CoreUC DavisOne Shields AveDavisCA95616USA
| | | | | | | | - John Van Sickle
- Department of Fisheries and WildlifeOregon State UniversityCorvallisOR97331USA
| | - Kathleen G. O'Malley
- Coastal Oregon Marine Experiment StationDepartment of Fisheries and WildlifeHatfield Marine Science CenterOregon State UniversityNewportOR97365USA
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14
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Validation of two canine STR multiplex-assays following the ISFG recommendations for non-human DNA analysis. Forensic Sci Int Genet 2013; 8:90-100. [PMID: 24315595 DOI: 10.1016/j.fsigen.2013.07.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 06/07/2013] [Accepted: 07/01/2013] [Indexed: 11/22/2022]
Abstract
To gain general acceptance forensic DNA testing in animals needs to improve standardization of analysis methods and data interpretation. Recently, the International Society of Forensic Genetics (ISFG) took particular care of this topic by publishing recommendations for forensic non-human DNA analysis following the successful example of human DNA analysis in order to provide a basis for harmonization of the still existing inter-laboratory variability. By following these recommendations we demonstrate the performance of two short tandem repeat (STR) multiplexes for forensic identity testing of canine biological material. Thirteen STRs and two sex-specific markers were selected and validated according to the ISFG guidelines. Population genetic parameters were calculated based on 295 dog samples collected in Austria (124) and Germany (171). A repeat-based nomenclature of the mainly tetrameric STRs and corresponding allelic ladders are presented. All 146 different alleles included in the ladders were sequenced for correct allele calling. Additionally, a canine cell line (DH82-D3167) was evaluated as standard reference material.
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15
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Sim YT, Na JG, Lee CS. Forensic Characterization of Four New Bovine Tri-nucleotide Microsatellite Markers in Korean Cattle (Hanwoo). JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2013. [DOI: 10.5187/jast.2013.55.2.87] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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16
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Nishimaki T, Ibi T, Tanabe Y, Miyazaki Y, Kobayashi N, Matsuhashi T, Akiyama T, Yoshida E, Imai K, Matsui M, Uemura K, Watanabe N, Fujita T, Saito Y, Komatsu T, Yamada T, Mannen H, Sasazaki S, Kunieda T. The assessment of genetic diversity within and among the eight subpopulations of Japanese Black cattle using 52 microsatellite markers. Anim Sci J 2013; 84:585-91. [PMID: 23607656 DOI: 10.1111/asj.12045] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 01/07/2013] [Indexed: 11/28/2022]
Abstract
Japanese Black cattle are at risk for genetic homogeneity due to intensive use of a few sires. Therefore, assessment of the actual genetic diversity of this breed is important for future breeding plans. In the present study, we investigated the genetic diversity within and among eight subpopulations of Japanese Black cattle using 52 microsatellite markers. The parameters for genetic diversity of Japanese Black cattle were comparable to those of other cattle breeds, suggesting that the relatively high genetic diversity of the breed. However, upon comparison among the eight subpopulations, the Hyogo subpopulation showed markedly low genetic diversity. The results of the pairwise FST values, phylogenetic network and structure analysis indicated that the Hyogo population has remarkably high level of genetic differentiation from other populations, while Yamagata, Niigata, Hiroshima and Kagawa populations have low levels of genetic differentiation. Furthermore, multidimensional scaling plots indicated that individuals in some subpopulations were separated from individuals in the other subpopulations. We conclude that while the overall genetic diversity of Japanese Black cattle is still maintained at a relatively high level, that of a particular subpopulation is significantly reduced, and therefore the effective population size of the breed needs to be controlled by correct mating strategies.
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Affiliation(s)
- Takahiro Nishimaki
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
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17
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Lenstra JA, Groeneveld LF, Eding H, Kantanen J, Williams JL, Taberlet P, Nicolazzi EL, Sölkner J, Simianer H, Ciani E, Garcia JF, Bruford MW, Ajmone-Marsan P, Weigend S. Molecular tools and analytical approaches for the characterization of farm animal genetic diversity. Anim Genet 2012; 43:483-502. [DOI: 10.1111/j.1365-2052.2011.02309.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2011] [Indexed: 12/30/2022]
Affiliation(s)
- J. A. Lenstra
- Faculty of Veterinary Medicine; Utrecht University; Utrecht; The Netherlands
| | - L. F. Groeneveld
- Institute of Farm Animal Genetics; Friedrich-Loeffler-Institut; Hoeltystr. 10; 31535; Neustadt; Germany
| | - H. Eding
- Animal Evaluations Unit; CRV; Arnhem; The Netherlands
| | - J. Kantanen
- Biotechnology and Food Research; MTT Agrifood Research Finland; FI-31600; Jokioinen; Finland
| | - J. L. Williams
- Parco Tecnologico Padano; via Einstein; 2600; Lodi; Italy
| | - P. Taberlet
- Laboratoire d'Ecologie Alpine; Université Joseph Fourier; BP 53; Grenoble; France
| | - E. L. Nicolazzi
- Istituto di Zootecnica and BioDNA Research Centre; Università Cattolica del Sacro Cuore; Piacenza; Italy
| | - J. Sölkner
- Department of Sustainable Agricultural Systems; Animal Breeding Group; BOKU - University of Natural Resources and Life Sciences; Vienna; Austria
| | - H. Simianer
- Department of Animal Sciences; Animal Breeding and Genetics Group; Georg-August-University Göttingen; 37075; Göttingen; Germany
| | - E. Ciani
- Department of General and Environmental Physiology; University of Bari “Aldo Moro”; Bari; Italy
| | - J. F. Garcia
- Universidade Estadual Paulista; Araçatuba; Brazil
| | - M. W. Bruford
- Organisms and Environment Division; School of Biosciences; Cardiff University; Cardiff; UK
| | - P. Ajmone-Marsan
- Istituto di Zootecnica and BioDNA Research Centre; Università Cattolica del Sacro Cuore; Piacenza; Italy
| | - S. Weigend
- Institute of Farm Animal Genetics; Friedrich-Loeffler-Institut; Hoeltystr. 10; 31535; Neustadt; Germany
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O'Donoghue LE, Rivest JP, Duval DL. Polymerase chain reaction-based species verification and microsatellite analysis for canine cell line validation. J Vet Diagn Invest 2011; 23:780-5. [PMID: 21908323 DOI: 10.1177/1040638711408064] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Cell line cross-contamination as well as genetic drift during passaging have been acknowledged as widespread problems since the 1960s. Improper cell line identification can invalidate results and, if not discovered, pollute the scientific community's body of knowledge with regard to cancer cell lines, their gene expression, and their drug susceptibilities. Despite the obvious need, validation of cell line identity is not yet widely required, and the problem persists. A highly sensitive polymerase chain reaction (PCR)-based approach and short tandem repeat (STR) profiling were used to examine the prevalence of inter- and intraspecies cell line contamination in a veterinary research setting. First, 60 cell lines from 6 laboratories were tested with multiplex species-specific PCR capable of identifying 6 commonly used species. Of these, 3 were determined to be misidentified by species. Second, to identify intraspecies contamination among canine cancer cell lines, 29 canine lines from 3 different laboratories were analyzed with STR fingerprinting. Using this methodology, 3 canine cell lines were determined to be misidentified or cross-contaminated by other canine cell lines. Finally, genetic drift was observed within 1 cell line obtained from different laboratories. These findings emphasize the importance of cell line validation as a critical component of "good cell culture practice." A database of the STR profiles obtained in the current study has been established for future comparison and validation of canine cell lines by investigators at Colorado State University and other institutions.
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Affiliation(s)
- Liza E O'Donoghue
- Animal Cancer Center, Department of Clinical Sciences, Colorado State University, 300 West Drake Road, Fort Collins, Colorado 80523, USA
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van de Goor LHP, van Haeringen WA, Lenstra JA. Population studies of 17 equine STR for forensic and phylogenetic analysis. Anim Genet 2011; 42:627-33. [DOI: 10.1111/j.1365-2052.2011.02194.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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